Searching for AIRR-Seq records

You can display multiple data sets for the same species where these are available: first select the species of interest, then check the datasets for that species that you wish to search. Usually these will correspond to individual loci. VDJbase uses an Excel-style approach to searching and browsing data: click on the little triangle to… Continue reading Searching for AIRR-Seq records

AIRR-Seq data: Allele Names

The Germline Genes page lists all alleles discovered in the data set(s). The Appearances column counts the number of individuals in which each allele is found. You can click on a number in the Appearances column to view a list of samples containing instances of the allele. Note that the number of samples may not… Continue reading AIRR-Seq data: Allele Names

AIRR-Seq data: Sample Names

VDJbase uses a structured name such as P1_I41_S1 to refer to each sample. The numbers following P, I and S are allocated serially by VDJbase. P indicates the project number. You can see a list of projects on the Explore Data page. I is followed by a number identifying the individual within that project, and… Continue reading AIRR-Seq data: Sample Names

Human IGK and IGL AIRR-Seq datasets added

This summer we added human IGK and IGL AIRR-Seq datasets to VDJbase. These comprise those of the IGH studies which also provided light chain sequencing. You can find details of the studies on the Explore Data page – select the required dataset at the top of the page to view statistics.

Allele Review Extended

OGRDB is now accepting V- and J- sequence inferences from the human BCR light and heavy chain. Analysis scripts and submission pages have been updated accordingly.

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Categorised as OGRDB_News

Citing VDJbase

If you use VDJbase in your work, please cite our paper: Aviv Omer, Or Shemesh, Ayelet Peres, Pazit Polak, Adrian J Shepherd, Corey T Watson, Scott D Boyd, Andrew M Collins, William Lees, Gur Yaari, VDJbase: an adaptive immune receptor genotype and haplotype database, Nucleic Acids Research, Volume 48, Issue D1, 08 January 2020, Pages D1051–D1056,… Continue reading Citing VDJbase